Research Interests

• Evolution, sequence alignment, and computational DNA analysis
• Machine learning and predictive models
• Complex adaptive systems and nonlinear dynamics
• Learning in machines and animals
• Syntactic structure of bird song

Publications:

Books:

1. Methods for Computational Gene Prediction (2007). Majoros WH.  Cambridge University Press.  430 pages.
   

Book Chapters:

1. Gene Prediction Methods (2009) Majoros WH, Ohler U.  In: Bioinformatics, Tools and Applications. Springer.  pp99-120.
2. Dynamic programming for gene finders. (2005). Majoros WH.  In: Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics.  Wiley. 
3. Automatic concept identification in biomedical literature. (2005). Majoros WH.  In: Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics.  Wiley.
   

Research Articles:

1. Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs (2010) Majoros WH & Ohler U.  PLoS Computational Biology.  In press.
   
2. Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome (2009). Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U. Genome Biol. 10:R73.
   
3. Complexity Reduction in Context-dependent DNA Substitution Models (2008) Majoros WH, Ohler U. Bioinformatics 25:185-82..
4. A viral microRNA functions as an ortholog of cellular miR-155 (2007) Gottwein et al. Nature 450:1096-1099.
   
5. Spatial preferences of microRNA targets in 3' untranslated regions (2007). Majoros W, Ohler U. BMC Genomics 8:152.
6. Advancing the State of the Art in Computational Gene Prediction (2007) Majoros W and Ohler U. Proceedings of KDECB / Benelearn '06, Springer-Verlag.
   
7. JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions (2006) Allen J, Majoros W, Pertea M, Salzberg S. Genome Biology.
   
8. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. (2006) Eisen, J et al. PLoS Biology. 4(9).
9. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. (2005) Neirman, W et al. Nature 438:1151-1156.
10. Efficient implementation of a generalized pair hidden Markov model for comparative gene finding. (2005). Majoros WH, Pertea M, Salzberg L.  Bioinformatics 21, 1782-1788. (pdf)
11. Efficient decoding algorithms for generalized hidden Markov model gene finders. (2005). Majoros W, Pertea M, Delcher A, Salzberg S.  BMC Bioinformatics 6:16.  (pdf).
12. Gene discovery in the Acanthamoeba castellanii genome. (2005).  Anderson IJ et al. (2005). Protist.
    
13. An empirical analysis of training protocols for probabilistic gene finders. (2004). Majoros W, Salzberg S.  BMC Bioinformatics 5:206. (original: pdf) (erratum: pdf) (corrected: pdf)
    
14. TIGRscan and GlimmerHMM : two open source ab initio eukaryotic gene finders. (2004). Majoros W, Pertea M, Salzberg S.  Bioinformatics 20, 2878-2879. (pdf)
15. The ENCODE (ENCyclopedia Of DNA Elements) Project. (2004). The ENCODE Project Consortium. Science 306, 636-640.
    
16. GlimmerM, Exonomy, and Unveil: Three ab initio Eukaryotic Genefinders. (2003). Majoros W, Pertea M, Antonescu C, Salzberg S. Nucleic Acids Research 31, 3601-3604. (pdf)
17. Assessment of genome-wide protein function classification for Drosophila melanogaster. (2003). Mi H, Vandergriff J, Campbell M, Marechania A, Majoros W, Lewis S, Thomas PD, Ashburner M. Genome Research 13, 2118-2128. (pdf)
18. Identification of Key Concepts in Biomedical Literature using a Modified Markov Heuristic. (2002). Bioinformatics 19, 402-407. (pdf)
19. Genomics and Natural Language Processing. (2002). Nature Reviews Genetics 3, 601. (pdf)
20. The Genome Sequence of the Malaria Mosquito Anopheles gambiae. (2002). Holt et al., Science 298, 129-149.
    
21. A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome. (2002). Mural et al., Science 296, 1661-1671.
22. Syntactic Structure in Birdsong: Memetic Evolution of Songs or Grammars? (2002). Majoros W, Journal of Memetics, vol 6. (html)
23. The sequence of the human genome. (2001). Venter et al.,  Science 291, 1304-1351. (html) (pdf)

Teaching:

• Computational Sequence Biology (Duke University, Spring 2010), w/ Uwe Ohler
• Computational Biology of Gene Regulation (Duke University, Fall 2006), w/ Uwe Ohler
• Computational Biology of Gene Regulation (Duke University, Spring 2008), w/ Uwe Ohler

Education